Biology subjects

Peterman, E.

Publications and source records attributed to Peterman, E..

16 recordsLinked to original sources

bioRxiv2026

Transcriptomic profiling identifies cellular and molecular transitions during Merkel cell regeneration

Skin exhibits a remarkable capacity for regeneration, which requires the coordinated reconstitution of diverse cell types and structures. Merkel cells are mechanosensory cells that detect gentle touch and develop in coordination with dermal appendages, yet Merkel cell regeneration remains incompletely understood. To investigate Merkel cell lineage dynamics during skin regeneration, we performed single-cell RNA sequencing of regenerating adult zebrafish skin after dermal appendage removal. We find that the regenerating Merkel cell lineage is heterogeneous and characterize molecular markers associated with Merkel cell subpopulations. Through cross-species analysis with mouse and human Merkel cells, we identify conserved elements of Merkel cell identity and function across vertebrates. Trajectory analysis reveals a continuous spectrum of transcriptional state transitions within the Merkel cell population, suggesting dynamic lineage progression during regeneration and involving an epithelial-to-mesenchymal-like transition. Finally, cell fate mapping and in vivo analysis identify a putative pool of cldna+ suprabasal keratinocyte progenitors that give rise to regenerating Merkel cells. Together, these findings establish a genome resource for studies of zebrafish skin regeneration and provide insights into Merkel cell heterogeneity, conservation, lineage relationships and regenerative dynamics.

developmental biology↗

bioRxiv2026

Dynein-microtubule forces drive nucleokinesis and transmigration in T cells

Beyond the mechanical capacity of canonical actomyosin-driven amoeboid motility in permissive extracellular environments, the nucleus becomes the principal barrier to T cell migration in confining tissues. We establish the dynein-microtubule (MT) force-transmission axis as an essential mechanism for nuclear translocation during confined T cell migration and transmigration. We argue that dynein acts both as a motor and as an F-actin-anchored force-transmission element (fulcrum), sliding MTs and the MT-coupled nucleus along the cell cortex to drive nucleokinesis and productive cell displacement. Dynein is the primary driver of nucleokinesis: its inhibition arrests nucleus movement independently of myosin II activity, while F-actin dynamics remain spatiotemporally decoupled from nuclear oscillations. During transmigration, dynein and actomyosin act cooperatively and non-redundantly, and only combined inhibition abolishes nuclear passage. Computational modeling demonstrates that dynein-mediated pulling, together with volume exclusion imposed by the nucleus, is sufficient to generate self-organized nuclear oscillations. Dynein inhibition in zebrafish Langerhans cells impairs protrusion dynamics in situ, identifying the dynein-MT axis as an evolutionarily conserved mechanobiological program. Collectively, these findings identify the dynein-MT mechanical unit as a potential target for engineering T cells with enhanced solid-tumor infiltration.

cell biology↗

bioRxiv2025

Microtubule-dependent cell polarity regulates skin-resident macrophage phagocytosis and directed cell migration

Immune cells rapidly respond to tissue damage through dynamic properties of the cytoskeleton. How microtubules control immune cell functions during injury responses remains poorly understood. Within skin, tissue-resident macrophages known as Langerhans cells use dynamic dendrites to surveil the epidermis for damage and migrate through a densely packed epithelium to wounds. Here, we use Langerhans cells within the adult zebrafish epidermis as a model to investigate roles for microtubules in immune cell tissue surveillance, phagocytosis, and directed migration. We describe microtubule organization within Langerhans cells, and show that depolymerizing the microtubule cytoskeleton alters dendrite morphology, debris engulfment, and migration efficiency. We find that the microtubule organizing center positions adjacent to engulfed debris and that its position correlates with navigational pathfinding during directed cell migration. Stabilizing microtubules prevents Langerhans cell motility during directed cell migration by impairing navigation around cellular obstacles. Collectively, our work demonstrates requirements for microtubules in the dynamic actions of tissue-resident macrophages during epithelial surveillance and wound repair.

cell biology↗

bioRxiv2024

Calcium dynamics of skin-resident macrophages during homeostasis and tissue injury

Immune cells depend on rapid changes in intracellular calcium activity to modulate cell function. Skin contains diverse immune cell types and is critically dependent on calcium signaling for homeostasis and repair, yet the dynamics and functions of calcium in skin immune cells remain poorly understood. Here, we characterize calcium activity in Langerhans cells, skin-resident macrophages responsible for surveillance and clearance of cellular debris after tissue damage. Langerhans cells reside in the epidermis and extend dynamic dendrites in close proximity to adjacent keratinocytes and somatosensory peripheral axons. We find that homeostatic Langerhans cells exhibit spontaneous and transient changes in calcium activity, with calcium flux occurring primarily in the cell body and rarely in the dendrites. Triggering somatosensory axon degeneration increases the frequency of calcium activity in Langerhans cell dendrites. By contrast, we show that Langerhans cells exhibit a sustained increase in intracellular calcium following engulfment of damaged keratinocytes. Altering intracellular calcium activity leads to a decrease in engulfment efficiency of keratinocyte debris. Our findings demonstrate that Langerhans cells exhibit context-specific changes in calcium activity and highlight the utility of skin as an accessible model for imaging calcium dynamics in tissue-resident macrophages. SIGNIFICANCE STATEMENTO_LICalcium activity in immune cells is thought to regulate cell function, but studies focusing on tissue-resident macrophages are limited. C_LIO_LISkin-resident macrophages known as Langerhans cells exhibit rapid and transient changes in calcium activity in homeostatic conditions, which can change depending on the type of tissue injury inflicted. Pharmacological perturbation of calcium activity leads to a decrease in Langerhans cell engulfment. C_LIO_LIThese findings suggest calcium activity is important for tissue surveillance by Langerhans cells. C_LI

cell biology↗

bioRxiv2024

DYF-5 regulates intraflagellar transport by affecting train turnaround

Intraflagellar transport (IFT) coordinates the transport of cargo in cilia and is essential for ciliary function. CILK1 has been identified as a key regulator of IFT. The mechanism by which it acts has, however, remained unclear. In this study, we use fluorescence imaging and single-molecule tracking in the phasmid cilia of live C. elegans to study the effect of the CILK1 homolog DYF-5 on the dynamics of the IFT. We show that in the absence of DYF-5, IFT components accumulate at the ciliary tip. kinesin-II is no longer restricted to the proximal segment of the cilium but is present all throughout the cilium, while its velocity is different from that of OSM-3. The frequency of IFT trains is reduced and in particular retrograde trains were rarely observed. In the absence of DYF-5, retrograde transport is vastly reduced, resulting in the accumulation of IFT components at the tip and depletion at the base. The latter results in impeded anterograde train assembly, resulting in fewer trains with irregular composition. Our results show that DYF-5 plays a key role in regulating the turnarounds of IFT trains at the ciliary tip.

molecular biology↗

bioRxiv2024

Resolving interface structure and local internal mechanics of mitotic chromosomes

The interface of chromosomes enables them to interact with the cell environment and is crucial for their mechanical stability during mitosis. Here, we use Atomic Force Microscopy (AFM) to probe the interface and local micromechanics of the highly condensed and complex chromatin network of native human mitotic chromosomes. Our AFM images provide detailed snapshots of chromatin loops and Sister-Chromatids Intertwines. A scaling analysis of these images reveals that the chromatin surface has fractal nature. AFM-based Force Spectroscopy and microrheology further show that chromosomes can resist severe deformations, elastically recovering their initial shape following two characteristic timescales. Localized indentations over the chromatids reveal that the spatially varying micromechanics of the chromatin network is largely governed by chromatin density. Together, our AFM investigation provides new insights into the structure and local mechanics of mitotic chromosomes, offering a toolbox for further characterization of complex biological structures, such as chromosomes, down to the nanoscale.

biophysics↗

bioRxiv2024

Sorting at ciliary base and ciliary entry of BBSome, IFT-B and IFT-A

Summary/AbstractAnterograde intraflagellar transport (IFT) trains, composed of IFT-B, IFT-A and BBSome subcomplexes, are responsible for transporting ciliary proteins into the cilium. How IFT subcomplexes reach the ciliary base and assemble into IFT trains is poorly understood. Here, we perform quantitative single-molecule imaging in C. elegans chemosensory cilia to uncover how IFT subcomplexes arrive at the base, organize in IFT trains, and enter the cilium. We find that BBSomes reach the base via diffusion where they either associate with assembling IFT trains or with the membrane surrounding the base. In contrast, IFT-B and IFT-A reach the base via directed transport on vesicles that stop at distinct locations near the base. Individual subcomplexes detach from the vesicles into a diffusive pool and associate to assembling trains. Our results indicate that the assembly of IFT trains is a step-wise process involving the subsequent incorporation of first IFT-B, then IFT-A and finally BBSomes.

molecular biology↗

bioRxiv2023

Rho-associated kinase regulates Langerhans cell morphology and responsiveness to tissue damage

Skin is often the first physical barrier to encounter invading pathogens and physical damage. Damage to the skin must be resolved quickly and efficiently to maintain organ homeostasis. Epidermal-resident immune cells known as Langerhans cells use dendritic protrusions to dynamically surveil the skin microenvironment, which contains epithelial keratinocytes and somatosensory peripheral axons. The mechanisms governing Langerhans cell dendrite dynamics and responses to tissue damage are not well understood. Using skin explants from adult zebrafish, we show that Langerhans cells maintain normal surveillance activity following axonal degeneration and use their dynamic dendrites to engulf small axonal debris. By contrast, a ramified-to-rounded shape transition accommodates the engulfment of larger keratinocyte debris. We find that Langerhans cell dendrites are richly populated with actin and sensitive to a broad spectrum actin inhibitor. We further show that Rho-associated kinase (ROCK) inhibition leads to elongated dendrites, perturbed clearance of large debris, and reduced Langerhans cell migration to tissue-scale wounds. Altogether, our work describes the unique dynamics of Langerhans cells and involvement of the ROCK pathway in immune cell responses to damage of varying magnitude.

cell biology↗

bioRxiv2022

A small excitation window allows long-duration imaging of OCR-2-associated vesicles in C. elegans sensory neurons

Single-particle imaging using laser-illuminated widefield epi-fluorescence microscopy is a powerful tool to investigate molecular processes in vivo. Performing high-quality single-molecule imaging in such biological systems, however, remains a challenge due to difficulties in controlling the number of fluorescing molecules, photobleaching, and the autofluorescence background. Here, we show that by exciting only a small, 5-15 {micro}m wide region in chemosensory neurons in live C. elegans, we can significantly improve the duration and quality of single-molecule imaging. Small-window illumination microscopy (SWIM) allows long-duration single-particle imaging since fluorescently labelled proteins are only excited upon entering the small excited area, limiting their photobleaching. Remarkably, we also find that using a small excitation window significantly improves the signal-to-background ratio of individual particles. With the help of theoretical calculations, we explain that the improved signal-to-background ratio is due to reduced background, mostly caused by out-of-focus autofluorescence. We demonstrate the potential of this approach by studying the dendritic transport of a ciliary calcium channel protein, OCR-2, in the chemosensory neurons of C. elegans. We reveal that OCR-2-associated vesicles are continuously transported back and forth along the length of the dendrite and can switch between directed and diffusive states. Furthermore, we perform single-particle tracking of OCR-2-associated vesicles to quantitatively characterize the transport dynamics. SWIM can be readily applied to other in vivo systems where intracellular transport or cytoskeletal dynamics occur in elongated protrusions, such as axons, dendrites, cilia, microvilli and extensions of fibroblasts.

biophysics↗

bioRxiv2022

Cell surface receptors TREM2, CD14 and integrin αMβ2 drive sinking engulfment in phosphatidylserine-mediated phagocytosis

Macrophages phagocytose and thereby eliminate a wide array of extracellular threats, ranging from antibody-coated bacteria to apoptotic cells. Precision modulation of phagocytosis has emerged as a therapeutic strategy across a range of diseases, but is limited by our incomplete understanding of how macrophages recognize, engulf, and respond to different phagocytic targets. Here, we undertook a systematic investigation of the morphological, biophysical and regulatory differences between two major types of phagocytosis: an immunostimulatory form of phagocytosis triggered by antibody-coated targets and an immunosuppressive form triggered by phosphatidylserine (PS)-coated targets. We confirmed classic observations that antibody-mediated phagocytosis involves the extension of thin actin-rich protrusions around the target, but find that PS-mediated phagocytosis involves an unexpected combination of filopodial probing, piecemeal phagocytosis and a distinct sinking mechanism of uptake. Using a genome-wide screening approach, we identified genes specifically required for each form of phagocytosis, including actin regulators, cell surface receptors and intracellular signaling molecules. Three cell surface receptors - TREM2, CD14 and integrin M{beta}2 - were revealed as essential for PS-mediated uptake. Strikingly, each receptor exhibited a distinct pattern of localization at the plasma membrane and contributed uniquely to the organization of the PS-dependent phagocytic cup. Overall, this work reveals divergent genetic requirements for the morphologically and mechanically distinct forms of PS-mediated and antibody-mediated phagocytosis, thereby informing therapeutic strategies for substrate-specific phagocytosis modulation.

cell biology↗

bioRxiv2022

Skin-resident immune cells engulf axonal debris in adult epidermis

Somatosensory neurons extend enormous peripheral axons to the skin, where they detect diverse environmental stimuli. Somatosensory peripheral axons are easily damaged due to their small caliber and superficial location. Axonal damage results in Wallerian degeneration, creating vast quantities of cellular debris that phagocytes must remove to maintain organ homeostasis. The cellular mechanisms that ensure efficient clearance of axon debris from stratified adult skin are unknown. Here, we establish zebrafish scales as a tractable model to study axon degeneration in the adult epidermis. Using this system, we demonstrate that skin-resident immune cells known as Langerhans cells engulf the majority of axon debris. In contrast to immature skin, adult keratinocytes do not significantly contribute to debris removal, even in animals lacking Langerhans cells. Our study establishes a powerful new model for studying Wallerian degeneration and identifies a new function for Langerhans cells in maintenance of adult skin homeostasis following injury. These findings have important implications for pathologies that trigger somatosensory axon degeneration.

cell biology↗

bioRxiv2020

Rapid diffusion of large TatA complexes detected using single particle tracking microscopy

The twin-arginine translocation (Tat) system transports folded proteins across the cytoplasmic membrane of most bacteria and archaea. TatA, which contains a single membrane-spanning helix, is believed to be responsible for the actual translocation. According to the prevalent model, multiple TatA subunits form a transient protein-conducting pore, which disassembles after each translocation event. An alternative model exists, in which TatA proteins locally weaken the lipid bilayer to translocate folded proteins. Here, we imaged eGFP-fused TatA expressed from the genome in live E. coli cells. Images showed TatA occuring both in highly mobile monomers or small oligomers and in large, stable complexes that do not dissociate. Single-particle tracking revealed that large TatA complexes switch between fast and slow diffusion. The fast diffusion is too fast for a transmembrane protein complex consisting of multiple TatA monomers. In line with recent data on rhomboid proteases, we propose that TatA complexes switch between a slowly diffusing transmembrane conformation and a rapidly diffusing membrane-disrupting state that enables folded proteins to cross the membrane, in accordance with the membrane-weakening model.

microbiology↗

bioRxiv2020

Rab14/MACF2/CAMSAP3 Complex Regulates Endosomal Targeting to the Abscission Site During Cytokinesis

Abscission is complex cellular process that is required for mitotic division. It is well-established that coordinated and localized changes in actin and microtubule dynamics are vital for cytokinetic ring formation, as well as establishment of the abscission site. Actin cytoskeleton reorganization during abscission would not be possible without the interplay between Rab11- and Rab35-containing endosomes and their effector proteins, whose roles in regulating endocytic pathways at the cleavage furrow have now been studied extensively. Here, we identified Rab14 as novel regulator of abscission. We demonstrate that depletion of Rab14 causes either cytokinesis failure or significantly prolongs division time. We show that Rab14 regulates the efficiency of recruiting Rab11-endosomes to the central spindle microtubules and that Rab14 knockout leads to inhibition of actin clearance at the abscission site. Finally, we demonstrate that Rab14 binds to microtubule minus-end interacting MACF2/CAMSAP3 complex and that this binding is required for targeting of early endosomes to the central spindle. Collectively, our data identified Rab14/MACF2/CAMSAP3 as a protein complex that regulates Rab11-endosome targeting and the establishment of the abscission site.

cell biology↗

bioRxiv2019

SRPK3 regulates alternative pre-mRNA splicing required for B lymphocyte development and humoral responsiveness

Alternative splicing (AS) of pre-mRNA is a critical component of transcriptional regulation that diversifies the cellular proteome. The Serine-Arginine Protein Kinases (SRPK) initiate early events in AS. Using conditional knockout mice (cKO), we demonstrated the importance of the X-linked gene Srpk3 in B lymphocyte development and in response to immunization in vivo. Significantly decreased numbers of immature and mature B cells were observed in Srpk3-cKO BM relative to wild-type (WT). Immunization of Srpk3-cKO mice with a T lymphocyte-independent type-2 antigen elicited greatly reduced amounts of specific IgG3. Srpk3 deletion resulted in hundreds of differentially spliced mRNAs in B cells, including mRNAs encoding proteins associated with signaling pathways and mitochondrial function. Several alternative splicing outcomes in Srpk3-cKO cells are due to altered splicing regulation of SR proteins. We conclude that Srpk3 is an immunomodulatory kinase that controls humoral immunity via its regulation of pre-mRNA splicing, antibody production, and metabolism in B cells.\n\nOne Sentence SummarySRPK3 regulates alternative splicing of pre-mRNA that is crucial for B cell development, activation and antibody responses.

immunology↗

bioRxiv2019

CLIC4, a new component of the cytokinetic ring, regulates actin cytoskeleton dynamics during the anaphase-to-telophase transition

During mitotic cell division, the actomyosin cytoskeleton undergoes several dynamic changes that play key roles in progression through mitosis. While the regulators of cytokinetic ring formation and contraction are well-established, proteins that regulate cortical stability during anaphase and telophase have been understudied. Here, we describe a role for CLIC4 in regulating actin and actin-regulators at the cortex and cytokinetic cleavage furrow during cytokinesis. We first describe CLIC4 as a new component of the cytokinetic cleavage furrow that is required for successful completion of mitotic cell division. We also demonstrate that CLIC4 regulates the remodeling of sub-plasma membrane actomyosin network within the furrow by recruiting MST4 kinase and regulating ezrin phosphorylation. This work identifies and characterizes new molecular players involved in the transition from the contracting cytokinetic ring to the intercellular bridge during cytokinesis.

cell biology↗

bioRxiv2019

Inhibiting IFT dynein with ciliobrevin in C. elegans chemosensory cilia

Cytoplasmic dyneins play a role in a myriad of cellular processes, such as retrograde intracellular transport and cell division. Small-molecule cytoplasmic dynein antagonists, ciliobrevins, have recently been developed as tools to acutely probe cytoplasmic dynein function. Although widely used to investigate cytoplasmic dynein 1, far fewer studies explore the effect of ciliobrevin on cytoplasmic dynein 2 or IFT dynein. Here, we use ciliobrevin A to partially disrupt IFT dynein in the chemosensory cilia of living C. elegans. Acute, low-concentration ciliobrevin treatment results in shortening of cilia and reduction of transport velocity in both directions. After longer exposure to ciliobrevin, we find concentration-dependent motor accumulations and axonemal deformations. We propose that maintenance of ciliary length requires a high fraction of active IFT-dynein motors, while structural integrity can be preserved by only a few active motors.

biophysics↗